Atomistry » Manganese » PDB 4b5i-4dec » 4d8f
Atomistry »
  Manganese »
    PDB 4b5i-4dec »
      4d8f »

Manganese in PDB 4d8f: Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)

Enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)

All present enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn):
1.17.4.1;

Protein crystallography data

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn), PDB code: 4d8f was solved by L.M.K.Dassama, A.K.Boal, C.Krebs, A.C.Rosenzweig, J.M.Bollinger Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.221, 97.998, 100.291, 90.00, 97.79, 90.00
R / Rfree (%) 18.6 / 23.5

Other elements in 4d8f:

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) (pdb code 4d8f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn), PDB code: 4d8f:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 1 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:36.8
occ:1.00
 OE1 A:GLU89 2.1 23.4 1.0
OE1 A:GLU120 2.2 19.3 1.0
ND1 A:HIS123 2.4 16.0 1.0
O A:HOH642 2.5 20.1 1.0
OE1 A:GLU227 2.9 28.8 1.0
FE A:FE401 3.1 38.4 1.0
CD A:GLU89 3.1 22.9 1.0
CE1 A:HIS123 3.1 15.4 1.0
CD A:GLU120 3.1 18.5 1.0
OE2 A:GLU120 3.4 20.4 1.0
OE2 A:GLU89 3.4 25.2 1.0
CG A:HIS123 3.5 15.5 1.0
CD A:GLU227 3.9 25.8 1.0
CE2 A:PHE197 4.0 21.1 1.0
CB A:HIS123 4.0 15.5 1.0
OE2 A:GLU227 4.2 26.6 1.0
NE2 A:HIS123 4.3 15.5 1.0
CG A:GLU89 4.4 20.4 1.0
CD2 A:PHE197 4.5 20.6 1.0
CG A:GLU120 4.5 16.2 1.0
CD2 A:HIS123 4.6 15.6 1.0
OE2 A:GLU193 4.6 22.1 1.0
CA A:GLU120 4.6 14.9 1.0
CE1 A:HIS230 4.6 15.4 1.0
CG2 A:ILE223 4.6 16.0 1.0
ND1 A:HIS230 4.7 13.9 1.0
CB A:GLU89 4.7 18.5 1.0
CB A:GLU120 4.8 14.8 1.0
CZ A:PHE197 4.9 20.7 1.0
CA A:GLU89 5.0 18.0 1.0

Manganese binding site 2 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 2 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:43.1
occ:1.00
 OE1 B:GLU89 2.0 27.8 1.0
OE1 B:GLU227 2.2 27.5 1.0
OE1 B:GLU120 2.3 23.6 1.0
O B:HOH573 2.4 39.9 1.0
ND1 B:HIS123 2.5 14.7 1.0
CD B:GLU89 3.0 25.8 1.0
FE B:FE402 3.1 45.5 1.0
CD B:GLU120 3.3 21.5 1.0
CD B:GLU227 3.3 27.3 1.0
CE1 B:HIS123 3.3 15.4 1.0
OE2 B:GLU89 3.4 27.3 1.0
OE2 B:GLU120 3.5 22.9 1.0
CG B:HIS123 3.6 15.2 1.0
CE2 B:PHE197 3.8 28.0 1.0
OE2 B:GLU227 3.9 28.8 1.0
CB B:HIS123 4.1 15.5 1.0
CG B:GLU227 4.3 22.8 1.0
CG B:GLU89 4.3 22.9 1.0
NE2 B:HIS123 4.5 15.0 1.0
CE1 B:HIS230 4.6 15.2 1.0
ND1 B:HIS230 4.6 15.2 1.0
CG B:GLU120 4.6 18.1 1.0
CB B:GLU89 4.6 21.0 1.0
CA B:GLU120 4.6 15.7 1.0
CZ B:PHE197 4.6 27.8 1.0
CD2 B:PHE197 4.6 27.7 1.0
CG2 B:ILE223 4.7 17.0 1.0
OE2 B:GLU193 4.7 24.8 1.0
CD2 B:HIS123 4.7 15.2 1.0
CA B:GLU89 4.9 20.5 1.0
CB B:GLU120 4.9 16.1 1.0

Manganese binding site 3 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 3 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:42.9
occ:1.00
 OE1 C:GLU89 2.0 30.5 1.0
OE1 C:GLU120 2.3 26.2 1.0
ND1 C:HIS123 2.4 17.8 1.0
OE1 C:GLU227 2.9 31.9 1.0
CD C:GLU89 3.1 28.6 1.0
FE C:FE401 3.1 47.1 1.0
CE1 C:HIS123 3.2 17.1 1.0
CD C:GLU120 3.3 23.9 1.0
OE2 C:GLU89 3.5 30.6 1.0
CG C:HIS123 3.6 18.6 1.0
OE2 C:GLU120 3.7 25.4 1.0
CD C:GLU227 3.8 30.3 1.0
CE2 C:PHE197 3.9 24.3 1.0
OE2 C:GLU227 4.0 31.5 1.0
CB C:HIS123 4.0 19.4 1.0
NE2 C:HIS123 4.4 18.6 1.0
CG C:GLU89 4.4 26.1 1.0
CD2 C:PHE197 4.4 25.2 1.0
CE1 C:HIS230 4.6 21.6 1.0
CD2 C:HIS123 4.6 17.4 1.0
CA C:GLU120 4.6 19.1 1.0
ND1 C:HIS230 4.6 21.3 1.0
CB C:GLU89 4.7 24.7 1.0
CG C:GLU120 4.7 20.9 1.0
CG2 C:ILE223 4.7 21.5 1.0
OE2 C:GLU193 4.8 28.5 1.0
CZ C:PHE197 4.8 24.6 1.0
CB C:GLU120 4.9 19.0 1.0
CA C:GLU89 5.0 24.3 1.0

Manganese binding site 4 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 4 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:43.9
occ:1.00
 OE1 D:GLU89 2.2 30.4 1.0
ND1 D:HIS123 2.3 18.4 1.0
OE1 D:GLU227 2.3 27.5 1.0
OE1 D:GLU120 2.4 24.1 1.0
CE1 D:HIS123 3.0 18.4 1.0
CD D:GLU89 3.2 29.5 1.0
FE D:FE401 3.2 48.4 1.0
CD D:GLU227 3.3 26.7 1.0
CD D:GLU120 3.4 22.9 1.0
OE2 D:GLU89 3.5 30.8 1.0
CG D:HIS123 3.5 17.5 1.0
OE2 D:GLU120 3.7 24.2 1.0
OE2 D:GLU227 4.0 28.2 1.0
CB D:HIS123 4.0 17.1 1.0
CE2 D:PHE197 4.1 27.9 1.0
CG D:GLU227 4.2 23.6 1.0
NE2 D:HIS123 4.2 18.7 1.0
CD2 D:HIS123 4.5 17.8 1.0
CG D:GLU89 4.5 26.6 1.0
CE1 D:HIS230 4.5 18.9 1.0
CG2 D:ILE223 4.5 19.8 1.0
ND1 D:HIS230 4.6 18.8 1.0
CD2 D:PHE197 4.7 28.4 1.0
CA D:GLU120 4.7 18.4 1.0
CG D:GLU120 4.8 20.4 1.0
CB D:GLU89 4.8 25.1 1.0
CZ D:PHE197 4.9 28.9 1.0
OE2 D:GLU193 4.9 26.8 1.0

Reference:

L.M.Dassama, A.K.Boal, C.Krebs, A.C.Rosenzweig, J.M.Bollinger. Evidence That the Beta Subunit of Chlamydia Trachomatis Ribonucleotide Reductase Is Active with the Manganese Ion of Its Manganese(IV)/Iron(III) Cofactor in Site 1. J.Am.Chem.Soc. V. 134 2520 2012.
ISSN: ISSN 0002-7863
PubMed: 22242660
DOI: 10.1021/JA211314P
Page generated: Sat Oct 5 18:59:07 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy